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Biblio
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BioNetModel
Y. Lu
,
Muller, M.
,
Smith, D.
,
Dutta, B.
,
Mourov, K.
,
Iadevaia, S.
,
Ruths, D.
,
Tseng, J. - T.
,
Yu, S.
,
Yu, Q.
,
Nakhleh, L.
,
Balazsi, G.
,
Donnelly, J.
,
Schurdak, M.
,
Morgan-Lappe, S.
,
Fesik, S.
,
Ram, P. T.
, and
Mills, G. B.
,
“
Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling
”
,
Oncogene
, vol. 30, pp. 4567-4577, 2011.
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Oncogene2011.pdf
(905.3 KB)
W. Zhou
and
Nakhleh, L.
,
“
The strength of chemical linkage as a criterion for pruning metabolic graphs
”
,
Bioinformatics
, vol. 27, no. 14, pp. 1957-1963, 2011.
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ZhouNakhleh-Bioinformatics11.pdf
(749.76 KB)
W. Zhou
and
Nakhleh, L.
,
“
Properties of metabolic graphs: Biological organization or representation artifacts?
”
,
BMC Bioinformatics
, vol. 12, p. 132, 2011.
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ZhouNakhleh-BMCBioinfo11.pdf
(1.08 MB)
D. Ruths
and
Nakhleh, L.
,
“
Deriving predictive models of signaling network dynamics from qualitative experimental data
”
, in
Proceedings of the 9th Annual International Conference on Computational Systems Biology
, 2010.
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RuthsNakhleh-CSB2010.pdf
(548.82 KB)
T. Ruths
,
Ruths, D.
, and
Nakhleh, L.
,
“
GS2: An efficiently computable measure of GO-based similarity of gene sets
”
,
Bioinformatics
, vol. 25, pp. 1178-1184, 2009.
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D. Ruths
,
Muller, M.
,
Tseng, J. T.
,
Nakhleh, L.
, and
Ram, P. T.
,
“
The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks
”
,
PLoS Computational Biology
, vol. 4, p. e1000005, 2008.
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D. Ruths
,
Nakhleh, L.
, and
Ram, P. T.
,
“
Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle
”
,
BMC Systems Biology
, vol. 2, p. 76, 2008.
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D. Ruths
,
Tseng, J. T.
,
Nakhleh, L.
, and
Ram, P. T.
,
“
De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis
”
, in
Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics
, 2007, vol. 4205, pp. 108-118.
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D. Ruths
,
Nakhleh, L.
,
Iyengar, M. S.
,
Reddy, S. A. G.
, and
Ram, P. T.
,
“
Graph-theoretic Hypothesis Generation in Biological Signaling Networks
”
,
Journal of Computational Biology
, vol. 13, pp. 1546-1557, 2006.
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N. Berestovsky
,
Fukui, R.
, and
Nakhleh, L.
,
“
On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks.
”
,
Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
. pp. 184-191, 2012.
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BerestovskyFukuiNakhleh.pdf
(2.77 MB)
W. Zhou
and
Nakhleh, L.
,
“
Convergent evolution of modularity in metabolic networks through different community structures
”
,
BMC Evolutionary Biology
, vol. 12, p. 181, 2012.
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ZhouNakhleh-BMCEvolBiol2012.pdf
(1.88 MB)
W. Zhou
and
Nakhleh, L.
,
“
Quantifying And Assessing the Effect of Chemical Symmetry in Metabolic Pathways
”
,
Journal of Chemical Information and Modeling
, vol. 52, pp. 2684-2696, 2012.
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ZhouNakhleh-JCIM2012.pdf
(2.66 MB)
N. Berestovsky
and
Nakhleh, L.
,
“
An Evaluation of Methods for Inferring Boolean Networks from Time-series Data
”
,
PLoS One
, vol. 8, p. e66031, 2013.
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BerestovskyNakhleh-PLoSOne13.pdf
(942.99 KB)
N. Berestovsky
,
Zhou, W.
,
Nagrath, D.
, and
Nakhleh, L.
,
“
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
”
,
PLoS Computational Biology
, vol. 9, no. 11, p. e1003306, 2013.
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BerestovskyEtAl13.pdf
(1.66 MB)
S. Iadevaia
,
Nakhleh, L.
,
Azencott, R.
, and
Ram, P. T.
,
“
Mapping network motif tunability and robustness in the design of synthetic signaling circuits
”
,
PLoS One
, vol. 9, no. 3, p. e91743, 2014.
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IadevaiaEtAl-PLoSOne14.pdf
(1.01 MB)
CancerGenomics
X. Fan
,
Zhou, W.
,
Chong, Z.
,
Nakhleh, L.
, and
Chen, K.
,
“
Towards accurate characterization of clonal heterogeneity based on structural variation
”
,
BMC Bioinformatics
, vol. 15, p. 299, 2014.
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FanEtAl2014.pdf
(2.04 MB)
Epidemiology
C. Than
,
Sugino, R.
,
Innan, H.
, and
Nakhleh, L.
,
“
Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data
”
,
Bioinformatics
, vol. 24, pp. i123-i131, 2008.
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S. Takuno
,
Kado, T.
,
Sugino, R. P.
,
Nakhleh, L.
, and
Innan, H.
,
“
Population genomics in bacteria: A case study of Staphylococcus aureus.
”
,
Molecular Biology and Evolution
, vol. 29, no. 2, pp. 797-800, 2012.
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TakunoEtAl-MBE11.pdf
(933.28 KB)
W. Zhou
and
Nakhleh, L.
,
“
Convergent evolution of modularity in metabolic networks through different community structures
”
,
BMC Evolutionary Biology
, vol. 12, p. 181, 2012.
Google Scholar
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ZhouNakhleh-BMCEvolBiol2012.pdf
(1.88 MB)
NetEvol
Y. Zhu
and
Nakhleh, L.
,
“
Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models
”
,
Workshop on Algorithms in Bioinformatics
, vol. LNBI 7534. pp. 57-68, 2012.
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ZhuNakhleh-WABI12.pdf
(1.53 MB)
Y. Zhu
,
Du, P.
, and
Nakhleh, L.
,
“
Gene Duplicability-Connectivity-Complexity Across Organisms and a Neutral Evolutionary Explanation
”
,
PLoS One
, vol. 7, no. 9, p. e44491, 2012.
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ZhuDuNakhleh.pdf
(217.94 KB)
W. Zhou
and
Nakhleh, L.
,
“
Convergent evolution of modularity in metabolic networks through different community structures
”
,
BMC Evolutionary Biology
, vol. 12, p. 181, 2012.
Google Scholar
BibTeX
RTF
Tagged
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RIS
ZhouNakhleh-BMCEvolBiol2012.pdf
(1.88 MB)
T. Ruths
and
Nakhleh, L.
,
“
ncDNA and drift drive binding site accumulation
”
,
BMC Evolutionary Biology
, vol. 12, p. 159, 2012.
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RuthsNakhleh-BMCEvolBiol2012.pdf
(659.08 KB)
T. Ruths
and
Nakhleh, L.
,
“
Neutral forces acting on intragenomic variability shape the E. coli regulatory network topology
”
,
Proceedings of the National Academy of Sciences
, vol. 110, no. 19, pp. 7754-7759, 2013.
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RuthsNakhleh-PNAS13.pdf
(2.57 MB)
T. Ruths
and
Nakhleh, L.
,
“
Boosting forward-time population genetic simulators through genotype compression
”
,
BMC Bioinformatics
, vol. 14, p. 192, 2013.
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RuthsNakhleh-BMCBioinfo13.pdf
(680.55 KB)
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